Proteome-wide systems analysis of a cellulosic biofuel-producing microbe

Fermentation of plant biomass by microbes like Clostridium phytofermentans recycles carbon globally and can make biofuels from inedible feedstocks. We analyzed C. phytofermentans fermenting cellulosic substrates by integrating quantitative mass spectrometry of more than 2500 proteins with measuremen...

Full description

Saved in:
Bibliographic Details
Published in:Molecular systems biology 2011-01, Vol.7 (1), p.461-n/a
Main Authors: Tolonen, Andrew C, Haas, Wilhelm, Chilaka, Amanda C, Aach, John, Gygi, Steven P, Church, George M
Format: Article
Language:English
Subjects:
Alcohol
Alcohols
Amines
Bacteria
Bacterial Proteins - analysis
Bacterial Proteins - metabolism
Bacterial Proteins - secretion
Bioconversion
Biodegradation
Biodiesel fuels
Biofuels
Biology
Biomass
Bioprocessing
Carbohydrates
Carbon
Carbon - metabolism
Carbon sources
Cell Adhesion
Cell surface
Cellulose
Cellulose - metabolism
Clostridium
Clostridium - cytology
Clostridium - enzymology
Clostridium - metabolism
Clostridium - physiology
Clostridium phytofermentans
Degradation
Dehydrogenases
Deuterium
Electron microscopy
Energy conservation
Engineers
Enzymatic activity
Enzymes
Ethanol
Extracellular enzymes
Fatty acids
Fermentation
Ferredoxin
Fuels
Genomes
Glucose - metabolism
Glycolysis
Hemicellulose
Hexose
Intracellular
Iron
Isotopes
Learning algorithms
Linear Models
Machine learning
Mass Spectrometry
Metabolic Networks and Pathways
Metabolism
Methylation
Microorganisms
Microscopy
Microscopy, Electron, Scanning
Motility
Organic chemistry
Oxidoreductase
Peptides
Plant biomass
Polysaccharides
Polysaccharides - metabolism
Protein expression
Proteins
Proteome - analysis
Proteome - metabolism
Proteome - secretion
Proteomes
Proteomics
Raw materials
Saccharides
Scientific imaging
Secretion
Solutes
Spectroscopy
Surface layers
Systems analysis
Systems Biology - methods
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:Fermentation of plant biomass by microbes like Clostridium phytofermentans recycles carbon globally and can make biofuels from inedible feedstocks. We analyzed C. phytofermentans fermenting cellulosic substrates by integrating quantitative mass spectrometry of more than 2500 proteins with measurements of growth, enzyme activities, fermentation products, and electron microscopy. Absolute protein concentrations were estimated using Absolute Protein EXpression (APEX); relative changes between treatments were quantified with chemical stable isotope labeling by reductive dimethylation (ReDi). We identified the different combinations of carbohydratases used to degrade cellulose and hemicellulose, many of which were secreted based on quantification of supernatant proteins, as well as the repertoires of glycolytic enzymes and alcohol dehydrogenases (ADHs) enabling ethanol production at near maximal yields. Growth on cellulose also resulted in diverse changes such as increased expression of tryptophan synthesis proteins and repression of proteins for fatty acid metabolism and cell motility. This study gives a systems‐level understanding of how this microbe ferments biomass and provides a rational, empirical basis to identify engineering targets for industrial cellulosic fermentation. Synopsis Cellulose is the world's most abundant renewable, biological energy source (Leschine, 1995). Microbial fermentation of cellulosic biomass could sustainably provide enough ethanol for 65% of US ground transportation fuel at current levels (Somerville, 2006). However, cellulose in plant biomass is packaged into a crystalline matrix, making biomass deconstruction a key roadblock to using it as a feedstock (Houghton et al, 2006). A promising strategy to overcome biomass recalcitrance is consolidated bioprocessing (Lynd et al, 2002), which uses microbes such as Clostridium phytofermentans to both secrete enzymes to depolymerize biomass and then ferment the resulting hexose and pentose sugars to a biofuel such as ethanol. The C. phytofermentans genome encodes 161 carbohydrate‐active enzymes (CAZy) including 108 glycoside hydrolases spread across 39 families (Cantarel et al, 2009), highlighting the elaborate set of enzymes needed to breakdown different cellulosic polysaccharides. Faced with the complexity of metabolizing biomass, systems biology strategies are needed to comprehensively identify which cellulolytic and metabolic enzymes are used to ferment different cellulosic substrat
ISSN:1744-4292
1744-4292
DOI:10.1038/msb.2010.116